SEARCH · Search PubMed
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Explore the source record for details and available documents.
A one-electron, silicon quantum capping potential for use in capping the dangling bonds formed by artificially limiting silicon clusters or surfaces is developed. The quantum capping potentials are general and can be used directly in any computational package that can handle effective core potentials. For silicon clusters and silicon surface models, we compared the results of traditional hydrogen atom capping with those obtained from capping with quantum capping potentials. The results clearly show that cluster and surface models capped with quantum capping potentials have ionization potentials, electron affinities, and highest occupied molecular orbital-lowest unoccupied molecular orbital gaps that are in very good agreement with those of larger systems. The silicon quantum capping potentials should be applied in cases where one wishes to model processes involving charges or low-energy excitations in silicon clusters and surfaces consisting of more than ca. 150 atoms.
We give a survey on the application of the chemical fragmentation concept in computer modelling of extended covalent systems. It will be stressed that information on molecular topology, as well as location and composition of the reaction centre allows the construction of a reasonable initial guess for the wave function and thus facilitates the solution of the Schrödinger equation. For systems, where the chemical changes are localised to a few atoms, while others play the role of essentially electrostatic perturbation, a partition into active site and environment is possible providing a background to hybrid quantum mechanical/molecular mechanical (QM/MM) methods. Full molecular orbital treatment of large covalent systems at the minimal basis, semiempirical level becomes possible in the frame of the fragment self-consistent field (FSCF) method which was developed in the past two decades in our laboratory. As an application, we discuss the hydride shift reaction step in xylose isomerase catalysis.
A hybrid quantum/classical path integral Monte Carlo (QC-PIMC) method for calculating the quantum free energy barrier for hydrogen transfer reactions in condensed phases is presented. In this approach, the classical potential of mean force along a collective reaction coordinate is calculated using umbrella sampling techniques in conjunction with molecular dynamics trajectories propagated according to a mapping potential. The quantum contribution is determined for each configuration along the classical trajectory with path integral Monte Carlo calculations in which the beads move according to an effective mapping potential. This type of path integral calculation does not utilize the centroid constraint and can lead to more efficient sampling of the relevant region of conformational space than free-particle path integral sampling. The QC-PIMC method is computationally practical for large systems because the path integral sampling for the quantum nuclei is performed separately from the classical molecular dynamics sampling of the entire system. The utility of the QC-PIMC method is illustrated by an application to hydride transfer in the enzyme dihydrofolate reductase. A comparison of this method to the quantized classical path and grid-based methods for this system is presented.
A method for calculating interaction parameters traditionally used in phase-equilibrium computations in low-molecular systems has been extended for the prediction of solvent activities of aromatic polymer solutions (polystyrene+methylcyclohexane). Using ethylbenzene as a model compound for the repeating unit of the polymer, the intermolecular interaction energies between the solvent molecule and the polymer were simulated. The semiempirical quantum chemical method AM1, and a method for sampling relevant internal orientations for a pair of molecules developed previously were used. Interaction energies are determined for three molecular pairs, the solvent and the model molecule, two solvent molecules and two model molecules, and used to calculated UNIQUAC interaction parameters, a(ij) and a(ji). Using these parameters, the solvent activities of the polystyrene 90,000 amu+methylcyclohexane system, and the total vapor pressures of the methylcyclohexane+ethylbenzene system were calculated. The latter system was compared to experimental data, giving qualitative agreement. Figure Solvent activities for the methylcylcohexane(1)+polystyrene(2) system at 316 K. Parameters aij (blue line) obtained with the AM1 method; parameters aij (pink line) from VLE data for the ethylbenzene+methylcyclohexane system. The abscissa is the polymer weight fraction defined as y2(x1)=(1mx1)M2/[x1M1+(1mx1)M2], where x1 is the solvent mole fraction and Mi are the molecular weights of the components.
Wigner crystallization of electrons in 2D quantum dots is reported. It proceeds in two stages: (i) via radial ordering of electrons on shells and (ii) freezing of the intershell rotation. The phase boundary of the crystal is computed in the whole temperature-density plane, and the influences of quantum effects and the particle number are analyzed.
This work outlines a new on-line database of quantum calculations for RNA catalysis (QCRNA) available via the worldwide web at http://theory.chem.umn.edu/QCRNA. The database contains high-level density functional calculations for a large range of molecules, complexes and chemical mechanisms important to phosphoryl transfer reactions and RNA catalysis. Calculations are performed using a strict, consistent protocol such that a wealth of cross-comparisons can be made to elucidate meaningful trends in biological phosphate reactivity. Currently, around 2000 molecules have been collected in varying charge states in the gas phase and in solution. Solvation was treated with both the PCM and COSMO continuum solvation models. The data can be used to study important trends in reactivity of biological phosphates, or used as benchmark data for the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations.
The structures of (PbS)n (n = 1-9) clusters are investigated with density functional theory at the B3LYP level. Various pseudopotential basis sets on lead and the 6-31+G basis set on sulfur were employed. Full geometry optimization and extensive searches of the potential energy surface were carried out for clusters with n = 1-6. We find that even small PbS clusters (n > 2) start to take on the characteristic features of the rock salt structure of solid-state PbS (galena). The origin of some of the structural aspects of these crystals is shown to be associated with the partial covalent nature of the Pb-S bond. The magnitude of the HOMO-LUMO gap oscillates with increasing size of the clusters, in agreement with the observed behavior of the corresponding UV absorption bands of ultrasmall PbS quantum dots. Direct conformation of this oscillation was found by CIS(D) calculations, for which the absorption with the largest oscillator strength oscillates as the clusters grow from PbS to (PbS)9.
In the retina of dusk-active European cockchafers, Melolontha melolontha, the linear polarization of downwelling light (skylight or light from the tree canopy) is detected by photoreceptors in upward-pointing ommatidia with maximal sensitivity at 520 nm in the green portion of the spectrum. To date no attempt has been made to answer the question of why these beetles detect polarization in the green. Here we present an atmospheric optical and receptor-physiological explanation of why longer wavelengths are advantageous for the perception of polarization of downwelling light under canopies illuminated by the setting sun. Our explanation focuses on illumination situations during sunset in canopied optical environments, because cockchafers are active at sunset and fly predominantly under canopies during their swarming, feeding, and mating periods. Using three simple atmospheric optical models, we computed the degree of linear polarization, the linearly polarized intensity of downwelling light, the quantum catch, and quantum catch difference between polarization detectors with orthogonal microvilli under canopies illuminated by the setting sun as functions of wavelength and solar zenith angle. Based upon these computations, we show that the green sensitivity of polarization detectors in M. melolontha is tuned to the high polarized intensity of downwelling light in the green under canopies during sunset, an optimal compromise between simultaneous maximization of the quantum catch and the quantum catch difference. We also briefly discuss how green-sensitive polarization detectors can function efficiently enough during the pre-feeding and egg-laying flights of cockchafers, which always occur prior to sunset and under the sky.
We demonstrate that a Paul trap made up of four conducting nanotubes is capable of trapping a single electron. In addition to the size, the major differences between such a nano-trap and its macroscopic analogue are that the electron is treated as a quantum object and that its effect ("back reaction") on the trapping device cannot be ignored. We computationally demonstrate focusing and trapping of an electronic wave packet, while fully accounting for the image charges induced by the electron on the nanotubes. The electron image charge interaction significantly affects the electron dynamics, and thus the trap stability. An (entangled) set of trapped electrons offers a number of advantages for quantum information processing.
A new multicoefficient correlation method (MCCM) is presented for the determination of accurate van der Waals interactions. The method utilizes a novel parametrization strategy that simultaneously fits to very high-level binding, Hartree-Fock and correlation energies of homo- and heteronuclear rare gas dimers of He, Ne, and Ar. The decomposition of the energy into Hartree-Fock and correlation components leads to a more transferable model. The method is applied to the krypton dimer system, rare gas-water interactions, and three-body interactions of rare gas trimers He3, Ne3, and Ar3. For the latter, a very high-level method that corrects the rare-gas two-body interactions to the total binding energy is introduced. A comparison with high-level CCSD(T) calculations using large basis sets demonstrates the MCCM method is transferable to a variety of systems not considered in the parametrization. The method allows dispersion interactions of larger systems to be studied reliably at a fraction of the computational cost, and offers a new tool for applications to rare-gas clusters, and the development of dispersion parameters for molecular simulation force fields and new semiempirical quantum models.
New features of molecular wires can be observed when they are irradiated by laser fields. These effects can be achieved by periodically oscillating fields but also by short laser pulses. The theoretical foundation used for these investigations is a density-matrix formalism where the full system is partitioned into a relevant part and a thermal fermionic bath. The derivation of a quantum master equation, either based on a time-convolutionless or time-convolution projection-operator approach, incorporates the interaction with time-dependent laser fields nonperturbatively and is valid at low temperatures for weak system-bath coupling. From the population dynamics the electrical current through the molecular wire is determined. This theory including further extensions is used for the determination of electron transport through molecular wires. As examples, we show computations of coherent destruction of tunneling in asymmetric periodically driven quantum systems, alternating currents and the suppression of the directed current by using a short laser pulse.
Pyrroloquinolinones, furocoumarin analogues, contain a divinilbenzene moiety, suggesting possible photoreactivity. Quantum mechanics calculations indicate that the pyrrole-side double bond exhibits strong photoreactivity, while the pyridone-side double bond is only poorly photoreactive. Intercalation models obtained by molecular mechanics calculations suggest that, in the cis-syn intercalation arrangement, the pyridone-side double bond is well aligned with the nearby thymine, supporting possible C4-cycloaddition with the 5,6 double bond of thymine, while the pyrrole-side double bond assumes an unfavourable position for photobinding. These data suggest that photoreaction between the pyridone-side and thymine double bonds may takes place, although with very low yield. Experimental evidence concerning DNA-photobinding exhibited by 2,6-dimethyl-9-methoxy-4H-pyrroloquinolinone (Compound I) confirms theoretical predictions. The formation of C4-cycloadducts between the pyridone side double bond and thymine also takes place with very low yield. Compound I shows marked BSA photobinding, suggesting that pyrroloquinolinones may photoreact with proteins. The three pyrroloquinolinones examined show high yields of singlet oxygen generation, suggesting that photobiological effects may be obtained through this photodynamic pathway, rather than through DNA photobinding.
The Schur basis on n d-dimensional quantum systems is a generalization of the total angular momentum basis that is useful for exploiting symmetry under permutations or collective unitary rotations. We present efficient {size poly[n,d,log(1/epsilon)] for accuracy epsilon} quantum circuits for the Schur transform, which is the change of basis between the computational and the Schur bases. Our circuits provide explicit efficient methods for solving such diverse problems as estimating the spectrum of a density operator, quantum hypothesis testing, and communicating without a shared reference frame. We thus render tractable a large series of methods for extracting resources from quantum systems and for numerous quantum information protocols.
Low signal-to-noise ratio (SNR) has been the main obstacle to multiple quantum-filtered 23Na imaging becoming an important technique for biologic and clinical applications. Through computer simulations and phantom experiments, we show that the SNR in 23Na imaging can be substantially improved by weighted signal averaging. Three-dimensional single quantum and triple quantum (TQ)-filtered 23Na images of an externalized rabbit kidney were collected with this technique. The TQ-filtered image did not show any signal when the animal was alive. However, upon sacrificing the animal, the renal cortex became clearly visible without any significant increase in signal from the medullary region. This increase in TQ-filtered signal in the renal cortex may be caused by an increased concentration of intracellular Na+ in the large intracellular space present herein, compared with the medulla. To our knowledge, this study represents the first example of three-dimensional TQ-filtered 23Na image of a biological sample.
A new method is presented for the calculation of the Molecular Electrostatic Potential (MEP) in large systems. Based on the mixed Quantum Mechanics/Molecular Mechanics (QM/MM) approach, the method assumes both a quantum and classical description for the molecule, and the calculation of the MEP in the space surrounding the molecule is made using this dual treatment. The MEP at points close to the molecule is computed using a full QM formalism, while a pure classical evaluation of the MEP is used for points located at large distances from the molecule. The algorithm allows the user to select the desired level of accuracy in the MEP, so that the definition of the regions where the MEP is computed at the classical or QM levels is adjusted automatically. The potential use of this QM/MM MEP in molecular modeling studies is discussed.
The interacting quantum atoms approach [IQA, as presented by Blanco et al., J. Chem. Theory Comput. 1, 1096 (2005)] is applied to standard hydrogen bonded dimers. IQA is an interpretation tool based on a real space energy decomposition scheme fully consistent with the quantum theory of atoms in molecules. It provides a partition of every physical term present in the Hamiltonian into atomic and interatomic contributions. The procedure is orbital-free and self-contained, needing neither external references nor artificial intermediate states. Binding is the result of a competition between the destabilizing deformations suffered by the interacting fragments upon interaction and the stabilizing interaction energy itself. According to IQA, there is no incompatibility between the prevalent electrostatic image of hydrogen bonded systems and that favoring important covalent contributions. Depending on how we gather the different energetic terms, we may recover electrostatic or covalent pictures from the same underlying quantum mechanical description. Our results show that the nonclassical contributions to hydrogen bonding are spatially localized, involving only the H atom and its two nearest neighbors. IQA is well suited as a comparative tool. Its thin energetic decomposition allows us to recover exactly (or to a very good approximation) the quantities of the most widely used energy decomposition schemes. Such a comparison sheds light on the virtues and faults of the different methods and on the origin of the 50 years old debate regarding the covalent/electrostatic nature of the hydrogen bond.
A deterministic method is described for performing three-dimensional (3D) photon transport calculations of a LINAC head and phantom/patient geometry to obtain dose distributions for therapy planning. The space, energy, and directional-dependent photon flux density is obtained by numerically solving the Boltzmann equation in general 3D geometry using the method of characteristics. The deterministic transport calculations use similar ray tracing routines as found in Monte Carlo (MC) codes. A special treatment is developed to better represent the impact of scattering from accelerator head components. Equations are presented for computing the water kerma distribution due to the uncollided and collided photon flux density field in the patient region. Kerma results obtained from the deterministic computation are compared to Monte Carlo values for a variety of source spectra and field sizes. The agreement for kerma values in the beam is usually within the MC uncertainties. It is concluded that the deterministic method is a rigorous, first-principles approach that could provide a superior alternative to Monte Carlo calculations for some types of problems. However additional development is needed to provide capability for 3D electron transport calculations.